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Crystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with 4NP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WXL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 20-30% PEG 400, 0.1M HEPES, 0.01M MAGNESIUM SULPHATE, 11% 1,6-HEXANEDIOL
Crystal Properties Matthews coefficient Solvent content 2.59 52.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.669 α = 90 b = 120.253 β = 89.96 c = 154.593 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300HE 2015-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.45 50 98.2 0.049 13.9 3.3 86170 -1.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.49 95.5 0.768 1.29 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3WXL 2.45 20 68998 3632 84.82 0.19872 0.19552 0.2011 0.2599 0.261 RANDOM 43.992
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.11 -0.45 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.05 r_dihedral_angle_3_deg 18.521 r_dihedral_angle_4_deg 18.115 r_dihedral_angle_1_deg 6.601 r_angle_refined_deg 1.346 r_angle_other_deg 0.798 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.05 r_dihedral_angle_3_deg 18.521 r_dihedral_angle_4_deg 18.115 r_dihedral_angle_1_deg 6.601 r_angle_refined_deg 1.346 r_angle_other_deg 0.798 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15812 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing